In situ DNA-hybridization chain reaction (HCR): A facilitated in situ HCR system for the detection of environmental microorganisms

Tsuyoshi Yamaguchi, Shuji Kawakami, Masashi Hatamoto, Hiroyuki Imachi, Masanobu Takahashi, Nobuo Araki, Takashi Yamaguchi, Kengo Kubota

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

In situ detection of microorganisms by fluorescence in situ hybridization (FISH) is a powerful tool for environmental microbiology, but analyses can be hampered by low rRNA content in target organisms, especially in oligotrophic environments. Here, we present a non-enzymatic, hybridization chain reaction (HCR)-based signal amplified in situ whole-cell detection technique (in situ DNA-HCR). The components of the amplification buffer were optimized to polymerize DNA amplifier probes for in situ DNA-HCR. In situ hybridization of initiator probes followed by signal amplification via HCR produced bright signals with high specificity and probe permeation into cells. The detection rates for Bacteria in a seawater sample and Archaea in anaerobic sludge samples were comparable with or greater than those obtained by catalyzed reporter deposition (CARD)-FISH or standard FISH. Detection of multiple organisms (Bacteria, Archaea and Methanosaetaceae) in an anaerobic sludge sample was achieved by simultaneous in situ DNA-HCR. In summary, in situ DNA-HCR is a simple and easy technique for detecting single microbial cells and enhancing understanding of the ecology and behaviour of environmental microorganisms in situ.

Original languageEnglish
Pages (from-to)2532-2541
Number of pages10
JournalEnvironmental microbiology
Volume17
Issue number7
DOIs
Publication statusPublished - 2015 Jul 1

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics

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